############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r scmeth -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data scmeth ### ############################################################################## ############################################################################## * checking for file 'scmeth/DESCRIPTION' ... OK * preparing 'scmeth': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'my-vignette.Rmd' using rmarkdown Loading required package: BSgenome Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:scmeth': coverage The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: rtracklayer snapshotDate(): 2022-02-22 loading from cache Quitting from lines 167-170 (my-vignette.Rmd) Error: processing vignette 'my-vignette.Rmd' failed with diagnostics: failed to load resource name: AH99012 title: UCSC RepeatMasker annotations (Apr2021) for Mouse (mm10) reason: error reading from connection --- failed re-building 'my-vignette.Rmd' SUMMARY: processing the following file failed: 'my-vignette.Rmd' Error: Vignette re-building failed. Execution halted